Quantification of random motility and chemotaxis bacterial transport coefficients using individual-cell and population-scale assays

Anomalous Collective Dynamics of Autochemotactic Populations

While the role of local interactions in nonequilibrium phase transitions is well studied, a fundamental understanding of the effects of long-range interactions is lacking. We study the critical dynamics of reproducing agents subject to autochemotactic interactions and limited resources. A renormalization group analysis reveals distinct scaling regimes for fast (attractive or repulsive) interactions; for slow signal transduction, the dynamics is dominated by a diffusive fixed point. Furthermore, we present a correction to the Keller-Segel nonlinearity emerging close to the extinction threshold and a novel nonlinear mechanism that stabilizes the continuous transition against the emergence of a characteristic length scale due to a chemotactic collapse.

Chemorepellent-Loaded Nanocarriers Promote Localized Interference of Escherichia coli Transport to Inhibit Biofilm Formation

To mitigate antimicrobial resistance, we developed polymeric nanocarrier delivery of the chemorepellent signaling agent, nickel, to interfere with Escherichia coli transport to a surface, an incipient biofilm formation stage. The dynamics of nickel nanocarrier (Ni NC) chemorepellent release and induced chemorepellent response required to effectively modulate bacterial transport for biofilm prevention were characterized in this work. Ni NCs were fabricated with the established Flash NanoPrecipitation method. NC size was characterized with dynamic light scattering. Measured with a zincon monosodium salt colorimetric assay, NC nickel release was pH-dependent, with 62.5% of total encapsulated nickel released at pH 7 within 0-15 min, competitive with rapid E. coli transport to the surface. Confocal laser scanning microscopy of E. coli (GFP-expressing) biofilm growth dynamics on fluorescently labeled Ni NC coated glass coupled with a theoretical dynamical criterion probed the biofilm prevention outcomes of NC design. The Ni NC coating significantly reduced E. coli attachment compared to a soluble nickel coating and reduced E. coli biomass area by 61% compared to uncoated glass. A chemical-in-plug assay revealed Ni NCs induced a chemorepellent response in E. coli. A characteristic E. coli chemorepellent response was observed away from the Ni NC coated glass over 10 μm length scales effective to prevent incipient biofilm surface attachment. The dynamical criterion provided semiquantitative analysis of NC mechanisms to control biofilm and informed optimal chemorepellent release profiles to improve NC biofilm inhibition. This work is fundamental for dynamical informed design of biofilm-inhibiting chemorepellent-loaded NCs promising to mitigate the development of resistance and interfere with the transport of specific pathogens.

Direct measurement of the aerotactic response in a bacterial suspension

Aerotaxis is the ability of motile cells to navigate toward oxygen. A key question is the dependence of the aerotactic velocity with the local oxygen concentration c. Here we combine simultaneous bacteria tracking and local oxygen concentration measurements using Ruthenium encapsulated in micelles to characterize the aerotactic response of Burkholderia contaminans, a motile bacterium ubiquitous in the environment. In our experiments, an oxygen gradient is produced by the bacterial respiration in a sealed glass capillary permeable to oxygen at one end, producing a bacterial band traveling toward the oxygen source. We compute the aerotactic response χ(c) both at the population scale, from the drift velocity in the bacterial band, and at the bacterial scale, from the angular modulation of the run times. Both methods are consistent with a power-law χ∝c^{-2}, in good agreement with existing models based on the biochemistry of bacterial membrane receptors.

Recent Developments in Bacterial Chemotaxis Analysis Based on the Microfluidic System

Bacterial motility in response to chemicals, also called bacterial chemotaxis, is a critical ability to search for the optimal environment to ensure the survival of bacterial species. Recent advances in microbiology have allowed the engineering of bacterial chemotactic properties. Conventional methods for characterizing bacterial motility are not able to fully monitor chemotactic behavior. Developments in microfluidic technology have enabled the designing of new experimental protocols in which spatiotemporal control of the cellular microenvironment can be achieved, and in which bacterial motility can be precisely and quantitatively measured and compared. This review provides an overview of recent developments of and new insights into microfluidic systems for chemotaxis assay.

Investigating the Physical Effects in Bacterial Therapies for Avascular Tumors

Tumor-targeting bacteria elicit anticancer effects by infiltrating hypoxic regions, releasing toxic agents and inducing immune responses. Although current research has largely focused on the influence of chemical and immunological aspects on the mechanisms of bacterial therapy, the impact of physical effects is still elusive. Here, we propose a mathematical model for the anti-tumor activity of bacteria in avascular tumors that takes into account the relevant chemo-mechanical effects. We consider a time-dependent administration of bacteria and analyze the impact of bacterial chemotaxis and killing rate. We show that active bacterial migration toward tumor hypoxic regions provides optimal infiltration and that high killing rates combined with high chemotactic values provide the smallest tumor volumes at the end of the treatment. We highlight the emergence of steady states in which a small population of bacteria is able to constrain tumor growth. Finally, we show that bacteria treatment works best in the case of tumors with high cellular proliferation and low oxygen consumption.

Modelling bacterial chemotaxis for indirectly binding attractants

In bacterial chemotaxis, chemoattractant molecules may bind either directly or indirectly with receptors within the cell periplasmic space. The indirect binding mechanism, which involves an intermediate periplasmic binding protein, has been reported to increase sensitivity to dilute attractant concentrations as well as range of response. Current mathematical models for bacterial chemotaxis at the population scale do not appear to take the periplasmic binding protein (BP) concentration or the indirect binding mechanics into account. We formulate an indirect binding extension to the existing Rivero equation for chemotactic velocity based on fundamental reversible enzyme kinetics. The formulated indirect binding expression accounts for the periplasmic BP concentration and the dissociation constants for binding between attractant and periplasmic BP, as well as between BP and chemoreceptor. We validate the indirect-binding model using capillary assay simulations of the chemotactic responses of E. coli to the indirectly-binding attractants maltose and AI-2. The predicted response agrees well with experimental data from a number of maltose capillary assay studies conducted in previous literature. The model is also able to achieve good agreement with AI-2 capillary assay data of one study out of two tested. The chemotactic response of E. coli towards AI-2 appears to be of higher complexity due to reports of variable periplasmic BP concentration as well as the low concentration of periplasmic BP relative to the total receptor concentration. Our current model is thus suitable for indirect binding chemotactic response systems with constant periplasmic BP concentration that is significantly larger than the total receptor concentration, such as the response of E. coli towards maltose. Further considerations may be taken into account to model the chemotactic response towards AI-2 with greater accuracy.

Swimming of bacterium Bacillus subtilis with multiple bundles of flagella

We characterize the bundle properties for three different strains of B. subtilis bacteria with various numbers of flagella. Our study reveals that, surprisingly, the number of bundles is independent of the number of flagella, and the formation of three bundles is always the most frequent case. We assume that this relates to the fact that different mutants have the same body length. There is no significant difference between the bundle width and length for distinct strains, but the projected angle between the bundles increases with the flagellar number. Furthermore, we find that the swimming speed is anti-correlated with the projected angle between the bundles, and the wobbling angle between the swimming direction and cell body increases with the number of flagella. Our findings highlight the impact of geometrical properties of bacteria such as body length and bundle configuration on their motility.

Video processing analysis for the determination and evaluation of the chemotactic response in bacterial populations

The aim of the present work was to design a methodology based on video processing to obtain indicators of bacterial population motility that allow the quantitative and qualitative analysis and comparison of the chemotactic phenomenon with different attractants in the agarose-in plug bridge method. Video image sequences were processed applying Shannon's entropy to the intensity time series of each pixel, which conducted to a final pseudo colored image resembling a map of the dynamic bacterial clusters. Processed images could discriminate perfectly between positive and negative attractant responses at different periods of time from the beginning of the assay. An index of spatial and temporal motility was proposed to quantify the bacterial response. With this index, this video processing method allowed obtaining quantitative information of the dynamic changes in space and time from a traditional qualitative assay. We conclude that this computational technique, applied to the traditional agarose-in plug assay, has demonstrated good sensitivity for identifying chemotactic regions with a broad range of motility.

Transducer like proteins of Campylobacter jejuni 81-176: role in chemotaxis and colonization of the chicken gastrointestinal tract

Transducer Like Proteins (Tlps), also known as methyl accepting chemotaxis proteins (MCP), enable enteric pathogens to respond to changing nutrient levels in the environment by mediating taxis toward or away from specific chemoeffector molecules. Despite recent advances in the characterization of chemotaxis responses in Campylobacter jejuni, the impact of Tlps on the adaptation of this pathogen to disparate niches and hosts is not fully characterized. The latter is particularly evident in the case of C. jejuni 81-176, a strain that is known to be highly invasive. Furthermore, the cytoplasmic group C Tlps (Tlp5, 6, and 8) were not extensively evaluated. Here, we investigated the role of C. jejuni 81-176 Tlps in chemotaxis toward various substrates, biofilm formation, in vitro interaction with human intestinal cells, and chicken colonization. We found that the Δtlp6 and Δtlp10 mutants exhibited decreased chemotaxis toward aspartate, whereas the Δtlp6 mutant displayed a decreased chemotaxis toward Tri-Carboxylic Acid (TCA) cycle intermediates such as pyruvate, isocitrate, and succinate. Our findings also corroborated that more than one Tlp is involved in mediating chemotaxis toward the same nutrient. The deletion of tlps affected important phenotypes such as motility, biofilm formation, and invasion of human intestinal epithelial cells (INT-407). The Δtlp8 mutant displayed increased motility in soft agar and showed decreased biofilm formation. The Δtlp8 and Δtlp9 mutants were significantly defective in invasion in INT-407 cells. The Δtlp10 mutant was defective in colonization of the chicken proximal and distal gastrointestinal tract, while the Δtlp6 and Δtlp8 mutants showed reduced colonization of the duodenum and jejunum. Our results highlight the importance of Tlps in C. jejuni's adaptation and pathobiology.

Quantitative analysis of chemotaxis towards toluene by Pseudomonas putida in a convection-free microfluidic device

Chemotaxis has been shown to be beneficial for the migration of soil-inhabiting bacteria towards industrial chemical pollutants, which they degrade. Many studies have demonstrated the importance of this microbial property under various circumstances; however, few quantitative analyses have been undertaken to measure the two essential parameters that characterize the chemotaxis of bioremediation bacteria: the chemotactic sensitivity coefficient χ(0) and the chemotactic receptor constant K(c). The main challenge to determine these parameters is that χ(0) and K(c) are coupled together in non-linear mathematical models used to evaluate them. In this study we developed a method to accurately measure these parameters for Pseudomonas putida in the presence of toluene, an important pollutant in groundwater contamination. Our approach uses a multilayer microfluidic device to expose bacteria to a convection-free linear chemical gradient of toluene that is stable over time. The bacterial distribution within the gradient is measured in terms of fluorescence intensity, and is then used to fit the parameters Kc and χ(0) with mathematical models. Critically, bacterial distributions under chemical gradients at two different concentrations were used to solve for both parameters independently. To validate the approach, the chemotaxis parameters of Escherichia coli strains towards α-methylaspartate were experimentally derived and were found to be consistent with published results from related work.

Analytical modeling and experimental characterization of chemotaxis in Serratia marcescens

This paper presents a modeling and experimental framework to characterize the chemotaxis of Serratia marcescens (S. marcescens) relying on two-dimensional and three-dimensional tracking of individual bacteria. Previous studies mainly characterized bacterial chemotaxis based on population density analysis. Instead, this study focuses on single-cell tracking and measuring the chemotactic drift velocity V(C) from the biased tumble rate of individual bacteria on exposure to a concentration gradient of l-aspartate. The chemotactic response of S. marcescens is quantified over a range of concentration gradients (10^{-3} to 5 mM/mm) and average concentrations (0.5 × 10(-3) to 2.5 mM). Through the analysis of a large number of bacterial swimming trajectories, the tumble rate is found to have a significant bias with respect to the swimming direction. We also verify the relative gradient sensing mechanism in the chemotaxis of S. marcescens by measuring the change of V(C) with the average concentration and the gradient. The applied full pathway model with fitted parameters matches the experimental data. Finally, we show that our measurements based on individual bacteria lead to the determination of the motility coefficient μ (7.25 × 10(-6) cm(2)/s) of a population. The experimental characterization and simulation results for the chemotaxis of this bacterial species contribute towards using S. marcescens in chemically controlled biohybrid systems.

Taxis toward hydrogen gas by Methanococcus maripaludis

Knowledge of taxis (directed swimming) in the Archaea is currently expanding through identification of novel receptors, effectors, and proteins involved in signal transduction to the flagellar motor. Although the ability for biological cells to sense and swim toward hydrogen gas has been hypothesized for many years, this capacity has yet to be observed and demonstrated. Here we show that the average swimming velocity increases in the direction of a source of hydrogen gas for the methanogen, Methanococcus maripaludis using a capillary assay with anoxic gas-phase control and time-lapse microscopy. The results indicate that a methanogen couples motility to hydrogen concentration sensing and is the first direct observation of hydrogenotaxis in any domain of life. Hydrogenotaxis represents a strategy that would impart a competitive advantage to motile microorganisms that compete for hydrogen gas and would impact the C, S and N cycles.

α-Fe2O3 nanocolumns and nanorods fabricated by electron beam evaporation for visible light photocatalytic and antimicrobial applications

Both Fe2O3 thin films and nanorod arrays are deposited using electron beam evaporation through normal thin film deposition and oblique angle deposition (OAD) and are characterized structurally, optically, and photocatalytically. The morphologies of the thin films are found to be arrays of very thin and closely packed columnar structures, while the OAD films are well-aligned nanorod arrays. All films were determined to be in the hematite phase (α-Fe2O3), as confirmed by both structural and optical characterization. Texture measurements indicate that films have similar growth modes where the [110] direction aligns with the direction of material growth. Under visible light illumination, the thin film samples were more efficient at photocatalytically degrading methylene blue, while the nanorod arrays were more efficient at inactivating E. coli O157:H7. The size of the targeted agent and the different film morphologies result in different reactant/surface interactions, which is the main factor that determines photoactivity. Furthermore, an analytic mathematical model of bacterial inactivation based on chemotactic bacterial diffusion and surface deactivation is developed to quantify and compare the inactivation rate of the samples. These results indicate that α-Fe2O3 nanorods are promising candidates for antimicrobial applications and are expected to provide insight into the development of better visible-light antimicrobial materials for food products and processing environments, as well as other related applications.

Impact of fluorochrome stains used to study bacterial transport in shallow aquifers on motility and chemotaxis of Pseudomonas species

One of the most common methods of tracking movement of bacteria in groundwater environments involves a priori fluorescent staining. A major concern in using these stains to label bacteria in subsurface injection-and-recovery studies is the effect they may have on the bacterium's transport properties. Previous studies investigated the impact of fluorophores on bacterial surface properties (e.g. zeta potential). However, no previous study has looked at the impact of fluorescent staining on swimming speed and chemotaxis. It was found that DAPI lowered the mean population swimming speed of Pseudomonas putida F1 by 46% and Pseudomonas stutzeri by 55%. DAPI also inhibited the chemotaxis in both strains. The swimming speeds of P. putida F1 and P. stutzeri were diminished slightly by CFDA/SE, but not to a statistically significant extent. CFDA/SE had no effect on chemotaxis of either strain to acetate. SYBR(®) Gold had no effect on swimming speed or the chemotactic response to acetate for either strain. This research indicates that although DAPI may not affect sorption to grain surfaces, it adversely affects other potentially important transport properties such as swimming and chemotaxis. Consequently, bacterial transport studies conducted using DAPI are biased to nonchemotactic conditions and do not appear to be suitable for monitoring the effect of chemotaxis on bacterial transport in shallow aquifers.

Three-dimensional chemotaxis model for a crawling neutrophil

Chemotactic cell migration is a fundamental phenomenon in complex biological processes. A rigorous understanding of the chemotactic mechanism of crawling cells has important implications for various medical and biological applications. In this paper, we propose a three-dimensional model of a single crawling cell to study its chemotaxis. A single-cell study of chemotaxis has an advantage over studies of a population of cells in that it provides a clearer observation of cell migration, which leads to more accurate assessments of chemotaxis. The model incorporates the surface energy of the cell and the interfacial interaction between the cell and substrate. The semi-implicit Fourier spectral method is applied to achieve high efficiency and numerical stability. The simulation results provide the kinetic and morphological traits of a crawling cell during chemotaxis.

Bacterial chemotaxis in linear and nonlinear steady microfluidic gradients

Diffusion-based microfluidic devices can generate steady, arbitrarily shaped chemical gradients without requiring fluid flow and are ideal for studying chemotaxis of free-swimming cells such as bacteria. However, if microfluidic gradient generators are to be used to systematically study bacterial chemotaxis, it is critical to evaluate their performance with actual quantitative chemotaxis tests. We characterize and compare three diffusion-based gradient generators by confocal microscopy and numerical simulations, select an optimal design and apply it to chemotaxis experiments with Escherichia coli in both linear and nonlinear gradients. Comparison of the observed cell distribution along the gradients with predictions from an established mathematical model shows very good agreement, providing the first quantification of chemotaxis of free-swimming cells in steady nonlinear microfluidic gradients and opening the door to bacterial chemotaxis studies in gradients of arbitrary shape.

Quantitative analysis of transverse bacterial migration induced by chemotaxis in a packed column with structured physical heterogeneity

A two-dimensional mathematical model was developed to simulate transport phenomena of chemotactic bacteria in a sand-packed column designed with structured physical heterogeneity in the presence of a localized chemical source. In contrast to mathematical models in previous research work, in which bacteria were typically treated as immobile colloids, this model incorporated a convective-like chemotaxis term to represent chemotactic migration. Consistency between experimental observation and model prediction supported the assertions that (1) dispersion-induced microbial transfer between adjacent conductive zones occurred at the interface and had little influence on bacterial transport in the bulk flow of the permeable layers and (2) the enhanced transverse bacterial migration in chemotactic experiments relative to nonchemotactic controls was mainly due to directed migration toward the chemical source zone. On the basis of parameter sensitivity analysis, chemotactic parameters determined in bulk aqueous fluid were adequate to predict the microbial transport in our intermediate-scale porous media system. Additionally, the analysis of adsorption coefficient values supported the observation of a previous study that microbial deposition to the surface of porous media might be decreased under the effect of chemoattractant gradients. By quantitatively describing bacterial transport and distribution in a heterogeneous system, this mathematical model serves to advance our understanding of chemotaxis and motility effects in granular media systems and provides insights for modeling microbial transport in in situ microbial processes.

Idling time of swimming bacteria near particulate surfaces contributes to apparent adsorption coefficients at the macroscopic scale under static conditions

Static capillary assays were performed to observe the distribution of Escherichia coli and several mutant strains at the interface between an aqueous solution and a Gelrite particulate suspension, used as a model porous medium. Motile smooth-swimming mutant bacteria (E. coli HCB437) accumulated at the interface, but did not penetrate very far into the Gelrite suspension. Motile wild-type bacteria (E. coli HCB1) penetrated much further than the smooth-swimming mutant, but did not accumulate to the same extent at the interface. Nonmotile tumbly mutant bacteria (E. coli HCB359) did not accumulate or penetrate to a significant degree. Computer simulations using a Monte Carlo algorithm, with input parameters based on bacterial swimming properties in static bulk aqueous systems, appeared to underestimate the bacterial idling time associated with solid surfaces. To account for physicochemical, biological and geometrical influences, an additional component of the bacterial idling time was included. The third component of the idling time was further analyzed semiquantitatively with a 1-D population-scale transport model with first-order association (k(on)) and dissociation (k(off)) adsorption-like kinetics. Computer simulation results suggested that this additional bacterial idling time not only increased the magnitudes of k(on) and k(off), but also enhanced the ratio of k(on) to k(off). This further implies that motile bacteria may tend to accumulate at the boundaries of low-permeable regions in groundwater systems, which is beneficial for bioremediation of residual contamination that may not be accessible by conventional remediation approaches.

Chemotaxis: how bacteria use memory

Bacterial chemotaxis represents one of the simplest and best studied examples of unicellular behavior. Chemotaxis allows swimming bacterial cells to follow chemical gradients in the environment by performing temporal comparisons of ligand concentrations. The process of chemotaxis in the model bacteriumEscherichia colihas been studied in great molecular detail over the past 40 years, using a large range of experimental tools to investigate physiology, genetics and biochemistry of the system. The abundance of quantitative experimental data enabled detailed computational modeling of the pathway and theoretical analyses of such properties as robustness and signal amplification. Because of the temporal mode of gradient sensing in bacterial chemotaxis, molecular memory is an essential component of the chemotaxis pathway. Recent studies suggest that the memory time scale has been evolutionary optimized to perform optimal comparisons of stimuli while swimming in the gradient. Moreover, noise in the adaptation system, which results from variations of the adaptation rate both over time and among cells, might be beneficial for the overall chemotactic performance of the population.

Transverse bacterial migration induced by chemotaxis in a packed column with structured physical heterogeneity

The significance of chemotaxis in directing bacterial migration toward contaminants in natural porous media was investigated under groundwater flow conditions. A laboratory-scale column, with a coarse-grained sand core surrounded by a fine-grained annulus, was used to simulate natural aquifers with strata of different hydraulic conductivities. A chemoattractant source was placed along the central axis of the column to model contaminants trapped in the heterogeneous subsurface. Chemotactic bacterial strains, Escherichia coli HCB1 and Pseudomonas putida F1, introduced into the column by a pulse injection, were found to alter their transport behaviors under the influence of the attractant chemical emanating from the central source. For E. coil HCB1, approximately 18% more of the total population relative to the control without attractant exited the column from the coarse sand layer due to the chemotactic effects of alpha-methylaspartate under an average fluid velocity of 5.1 m/d. Although P. putida F1 demonstrated no observable changes in migration pathways with the model contaminant acetate under the same flow rate, when the flow rate was reduced to 1.9 m/d, approximately 6-10% of the population relative to the control migrated from the fine sand layer toward attractant into the coarse sand layer. Microbial transport properties were further quantified by a mathematical model to examine the significance of bacterial motility and chemotaxis under different hydrodynamic conditions, which suggested important considerations for strain selection and practical operation of bioremediation schemes.

Surface association of motile bacteria at granular porous media interfaces

Bacterial populations were observed using dark-field light scattering at porous media interfaces comprised of a dilute solution containing the polymer additives methylcellulose and a transparent particulate suspension composed of mechanically agitated Gelrite gellan gum. Population-scale experiments with a nonchemotactic smooth-swimming mutant, Escherichia col HCB 437, yielded a variety of distinct and reproducible bacterial distributions that included highly concentrated bands of bacteria near the interface. While no physical attachment was observed between the bacteria and granular Gelrite media, the population exhibited surface associations characterized by reversible physical obstructions of the motile bacteria at the solid granular surfaces. These interactions decreased translational motion, which reduced bacterial migration and concentrated bacterial populations near the interface. Results from glass bead experiments indicated similar surface associations in high-surface area glass bead environments. Experimental results were semiquantitatively analyzed using a one-dimensional population-scale transport model. Theoretical profiles were generated using a single set of parameters and simultaneously compared with averaged bacterial distributions from multiple interface configurations. Parameter estimates were consistent with expected values. The agreement between the theoretical and experimental data suggests a quantifiable approach for modeling bacterial migration within high-surface area granular media environments.

Enhanced transverse migration of bacteria by chemotaxis in a porous T-sensor

Subsurface bioremediation is often hindered by the inability to achieve good mixing between injected bacteria and residual contaminants. Chemotaxis, which is the ability of bacteria to migrate preferentially toward higher concentrations of certain chemical attractants, could potentially increase bacterial transport into the contaminated zone. To observe and quantify this chemotactic enhancement to bacterial dispersion transverse to groundwater flow, a microfluidic device--a porous T-sensor-was created. It allowed two streams of equal flow rate to enter side-by-side into a porous channel; the transverse mixing of the two streams was controlled primarily by dispersion. When a suspension of the chemotactic bacteria Escherichia coli HCB1 and a solution of chemical attractant alpha-methylaspartate were injected as the two incoming streams, enhanced bacterial migration into the attractant stream was observed relative to a control experiment with dispersion alone. Chemotaxis was observed under lower flow rates comparable to natural groundwaterflow. The chemotactic response was greater than that predicted by an advection-dispersion equation model using a chemotactic coefficient derived under quiescent experimental conditions, which suggests that flow in porous media may further enhance transverse migration for chemotactic bacteria. This study provided direct evidence of the significance of bacterial chemotactic transverse migration at groundwater flow rates.

Dependence of bacterial chemotaxis on gradient shape and adaptation rate

Simulation of cellular behavior on multiple scales requires models that are sufficiently detailed to capture central intracellular processes but at the same time enable the simulation of entire cell populations in a computationally cheap way. In this paper we present RapidCell, a hybrid model of chemotactic Escherichia coli that combines the Monod-Wyman-Changeux signal processing by mixed chemoreceptor clusters, the adaptation dynamics described by ordinary differential equations, and a detailed model of cell tumbling. Our model dramatically reduces computational costs and allows the highly efficient simulation of E. coli chemotaxis. We use the model to investigate chemotaxis in different gradients, and suggest a new, constant-activity type of gradient to systematically study chemotactic behavior of virtual bacteria. Using the unique properties of this gradient, we show that optimal chemotaxis is observed in a narrow range of CheA kinase activity, where concentration of the response regulator CheY-P falls into the operating range of flagellar motors. Our simulations also confirm that the CheB phosphorylation feedback improves chemotactic efficiency by shifting the average CheY-P concentration to fit the motor operating range. Our results suggest that in liquid media the variability in adaptation times among cells may be evolutionary favorable to ensure coexistence of subpopulations that will be optimally tactic in different gradients. However, in a porous medium (agar) such variability appears to be less important, because agar structure poses mainly negative selection against subpopulations with low levels of adaptation enzymes. RapidCell is available from the authors upon request.

Experimental verification of the behavioral foundation of bacterial transport parameters using microfluidics

We present novel microfluidic experiments to quantify population-scale transport parameters (chemotactic sensitivity chi(0) and random motility mu) of a population of bacteria. Previously, transport parameters have been derived theoretically from single-cell swimming behavior using probabilistic models, yet the mechanistic foundations of this upscaling process have not been verified experimentally. We designed a microfluidic capillary assay to generate and accurately measure gradients of chemoattractant (alpha-methylaspartate) while simultaneously capturing the swimming trajectories of individual Escherichia coli bacteria using videomicroscopy and cell tracking. By measuring swimming speed and bias in the swimming direction of single cells for a range of chemoattractant concentrations and concentration gradients, we directly computed the chemotactic velocity VC and the associated chemotactic sensitivity chi(0). We then show how mu can also be readily determined using microfluidics but that a population-scale microfluidic approach is experimentally more convenient than a single-cell analysis in this case. Measured values of both chi(0) [(12.4 +/- 2.0) x 10(-4) cm(2) s(-1)] and mu [(3.3 +/- 0.8) x 10(-6) cm(2) s(-1)] are comparable to literature results. This microscale approach to bacterial chemotaxis lends experimental support to theoretical derivations of population-scale transport parameters from single-cell behavior. Furthermore, this study shows that microfluidic platforms can go beyond traditional chemotaxis assays and enable the quantification of bacterial transport parameters.

A simple immune system simulation reveals optimal movement and cell density parameters for successful target clearance

We report here a simple simulation of the immune system in which we analysed the behaviour of responder cells in the presence of target cells. Variable parameters determined the behaviour of the cells within the simulation, and many simulations using the same parameters ensured that statistical variability was achieved. The model demonstrated that high mobility of the target or responder cells produced a more robust response, and that clearance by the immune system was favoured when effector cells moved rapidly compared with the target cells. Therefore, the high motility coefficients exhibited by T cells studied in vivo may play a role in optimizing the effector response to pathogens. Surprisingly, when the number density of responding cells was increased, target cell numbers were limited more effectively, but there was an increased likelihood of a prolonged response.

Assessment of sperm chemokinesis with exposure to jelly coats of sea urchin eggs and resact: a microfluidic experiment and numerical study

Specific peptides contained within the extracellular layer, or jelly coat,of a sea urchin egg have been hypothesized to play an important role in fertilization, though separate accounting of the effects of chemoattraction,chemokinesis, sperm agglomeration and the other possible roles of the jelly coat have not been reported. In the present study, we used a microfluidic device that allowed determination of the differences in the diffusion coefficients of sperm of the purple sea urchin Arbacia punctulatasubjected to two chemoattractants, namely the jelly coat and resact. Our objectives were twofold: (1) to experimentally determine and compare the diffusion coefficients of Arbacia punctulata spermatozoa in seawater,jelly coat solution and resact solution; and (2) to determine the effect of sea urchin sperm diffusion coefficient and egg size on the sperm–egg collision frequency using stochastic simulations. Numerical values of the diffusion coefficients obtained by diffusing the spermatozoa in seawater,resact solution and jelly coat solution were used to quantify the chemotactic effect. This allowed direct incorporation of known enlargements of the egg,and altered sperm diffusion coefficients in the presence of chemoattractant,in the stochastic simulations. Simulation results showed that increase in diffusion coefficient values and egg diameter values increased the collision frequency. From the simulation results, we concluded that type of sperm, egg diameter and diffusion coefficient are significant factors in egg fertilization. Increasing the motility of sperm appears to be the prominent role of the jelly coat.

Monte Carlo simulations derived from direct observations of individual bacteria inform macroscopic migration models at granular porous media interfaces

Motile bacteria accumulated at the interface between an aqueous solution and a polymer gel suspension. The gel suspension was produced using Gelrite and contained 50-500 microm semisolid gel particulates in aqueous buffer. Smooth-swimming (HCB437) and wild-type (HCB1) Escherchia coli displayed normal swimming behaviors in the aqueous buffer but exhibited no translational motion when obstructed by the semisolid particulates of the gel suspension. Translational motion immediately resumed after the bacteria reoriented in a direction away from the particle surfaces. These observations were incorporated into Monte Carlo simulations that linked individual swimming properties to macroscopic bacterial distributions. The simulations suggested that the apparent surface area of the porous media influenced the degree of bacteria/surface interactions and thatthe mechanism of surface association could concentrate bacterial populations based upon the physical constraints of the porous media system. Population distributions from the Monte Carlo simulations matched a 1-D transport model that characterized the bacteria/surface interactions as an adsorption-like process even though direct observations suggested no physical attachment was occurring. Consequently, the 1-D transport model provided a semiquantitative approach to approximate bacterial migrations within porous media systems. Results suggest that the self-propulsive nature of bacteria can produce nondiffusive migration patterns within high-surface area environments.

Effect of fungal hyphae on the access of bacteria to phenanthrene in soil

The effect of fungal hyphae on the mobilization of soil-dwelling bacteria and their access to hydrophobic phenanthrene in soil was tested in columns containing air-filled agricultural soil. The experimental design included a spatial separation between zones of bacterial inoculation and contamination. Motile Pseudomonas putida PpG7 (NAH7) and fast-growing, hydrophilic Pythium ultimum were used as the model phenanthrene-degrading and vector organisms, respectively. Efficient translocation of strain PpG7 in the range of centimetres in presence of P. ultimum indicated that the fungal mycelia bridged air-filled pores and thereby provided a continuous network of water-paths that enabled bacteria to spread in the soil. Biodegradation of the soil-associated phenanthrene was found only in the presence of the fungal mycelia, hence proving that the fungal network facilitated the access of the bacteria to the contaminant. Our data suggest that the specific stimulation of indigenous fungi is a promising method to mobilize pollutant degrading bacteria and thereby improve soil bioremediation in-situ.

Collective bacterial dynamics revealed using a three-dimensional population-scale defocused particle tracking technique

An ability to monitor bacterial locomotion and collective dynamics is crucial to our understanding of a number of well-characterized phenotypes including biofilm formation, chemotaxis, and virulence. Here, we report the tracking of multiple swimming Escherichia coli cells in three spatial dimensions and at single-cell resolution using a novel three-dimensional (3D) defocused particle tracking (DPT) method. The 3D trajectories were generated for wild-type Escherichia coli strain RP437 as well as for isogenic derivatives that display smooth swimming due to a cheA deletion (strain RP9535) or incessant tumbling behavior due to a cheZ deletion (strain RP1616). The 3D DPT method successfully differentiated these three modes of locomotion and allowed direct calculation of the diffusion coefficient for each strain. As expected, we found that the smooth swimmer diffused more readily than the wild type, and both the smooth swimmer and the wild-type cells exhibited diffusion coefficients that were at least two orders of magnitude larger than that of the tumbler. Finally, we found that the diffusion coefficient increased with increasing cell density, a phenomenon that can be attributed to the hydrodynamic disturbances caused by neighboring bacteria.

A three-channel microfluidic device for generating static linear gradients and its application to the quantitative analysis of bacterial chemotaxis

We have developed a prototype three-channel microfluidic chip that is capable of generating a linear concentration gradient within a microfluidic channel and is useful in the study of bacterial chemotaxis. The linear chemical gradient is established by diffusing a chemical through a porous membrane located in the side wall of the channel and can be established without through-flow in the channel where cells reside. As a result, movement of the cells in the center channel is caused solely by the cells chemotactic response and not by variations in fluid flow. The advantages of this microfluidic chemical linear gradient generator are (i) its ability to produce a static chemical gradient, (ii) its rapid implementation, and (iii) its potential for highly parallel sample processing. Using this device, wildtype Escherichia coli strain RP437 was observed to move towards an attractant (e.g., l-asparate) and away from a repellent (e.g., glycerol) while derivatives of RP437 that were incapable of motility or chemotaxis showed no bias of the bacteria's distribution. Additionally, the degree of chemotaxis could be easily quantified using this assay in conjunction with fluorescence imaging techniques, allowing for estimation of the chemotactic partition coefficient (CPC) and the chemotactic migration coefficient (CMC). Finally, using this approach we demonstrate that E. coli deficient in autoinducer-2-mediated quorum sensing respond to the chemoattractant l-aspartate in a manner that is indistinguishable from wildtype cells suggesting that chemotaxis is insulated from this mode of cell-cell communication.

Salmonella typhimurium specifically chemotax and proliferate in heterogeneous tumor tissue in vitro

Multi-drug resistance greatly limits the efficacy of conventional blood-born chemotherapeutics, which have limited ability to penetrate tumor tissue and are ineffective at killing quiescent cells far from tumor vasculature. Nonpathogenic, motile bacteria can overcome both of theses limitations. We hypothesize that the accumulation of S. typhimurium in tumors is controlled by two mechanisms: (1) chemotaxis towards compounds produced by quiescent cancer cells and (2) preferential growth within tumor tissue. We tested this hypothesis by quantifying the relative contributions of these mechanisms using the tumor cylindroid model, which mimics the microenvironments of in vivo tumors. Time-lapse fluorescence microscopy was used to measure the accumulation of GFP-labeled S. typhimurium into cylindroids of different size. Cylindroids larger than 500 microm in diameter contain quiescent cells, whereas cylindroids smaller than 500 microm do not. Spatio-temporal profiles of bacterial concentration were fit to a mathematical model to calculate two parameters that describe bacterial interaction with tumors: intratumoral bacterial growth, M, and intratumoral bacterial chemoattraction, K. It was observed that S. typhimurium is attracted to cylindroids and accumulate at long time points in the central region of large cylindroids. Both intratumoral bacterial growth and chemotaxis were significantly greater in large cylindroids, suggesting that quiescent cells secrete bacterial chemoattractants and the presence of necrotic and quiescent cells enable S. typhimurium to replicate in tumor tissue. In this study, several mechanisms of S. typhimurium accumulation in solid tumors have been quantified, which we believe is an important step in the development of bacterial-based therapeutics to target tumor quiescence.

Taking the fungal highway: mobilization of pollutant-degrading bacteria by fungi

The capacity of fungi to serve as vectors for the dispersion of pollutant-degrading bacteria was analyzed in laboratory model systems mimicking water-saturated (agar surfaces) and unsaturated soil environments (glass-bead-filled columns). Two common soil fungi (Fusarium oxysporum and Rhexocercosporidium sp.) forming hydrophilic and hydrophobic mycelia, respectively, and three polycyclic aromatic hydrocarbon degrading bacteria (Achromobacter sp. SK1, Mycobacterium frederiksbergense LB501TG, and Sphingomonas sp. L138) were selected based on the absence of mutual antagonistic effects. It was shown that fungal hyphae act as vectors for bacterial transport with mobilization strongly depending on the specific microorganisms chosen: The motile strain Achromobacter sp. SK1 was most efficiently spread along hyphae of hydrophilic F. oxysporum in both model systems with transport velocities of up to 1 cm d(-1), whereas no dispersion of the two nonmotile strains was observed in the presence of F. oxysporum. By contrast, none of the bacteria was mobilized along the hydrophobic mycelia of Rhexocercosporidium sp. growing on agar surfaces. In column experiments however, strain SK1 was mobilized by Rhexocercosporidium sp. It is hypothesized that bacteria may move by their intrinsic motilitythrough continuous (physiological) liquid films forming around fungal hyphae. The results of this study suggest that the specific stimulation of indigenous fungi may be a strategy to mobilize pollutant-degrading bacteria leading to their homogenization in polluted soil thereby improving bioremediation.

Continuous-flow capillary assay for measuring bacterial chemotaxis

Bacterial chemotaxis may have a significant impact on the structure and function of bacterial communities. Quantification of chemotactic motion is necessary to identify chemoeffectors and to determine the bacterial transport parameters used in predictive models of chemotaxis. When the chemotactic bacteria consume the chemoeffector, the chemoeffector gradient to which the bacteria respond may be significantly perturbed by the consumption. Therefore, consumption of the chemoeffector can confound chemotaxis measurements if it is not accounted for. Current methods of quantifying chemotaxis use bacterial concentrations that are too high to preclude chemoeffector consumption or involve ill-defined conditions that make quantifying chemotaxis difficult. We developed a method of quantifying bacterial chemotaxis at low cell concentrations ( approximately 10(5) CFU/ml), so metabolism of the chemoeffector is minimized. The method facilitates quantification of bacterial-transport parameters by providing well-defined boundary conditions and can be used with volatile and semivolatile chemoeffectors.

A high-throughput capillary assay for bacterial chemotaxis

We present a high-throughput capillary assay in order to characterize the chemotactic response of the E. coli bacterium. We measure the number of organisms attracted into an array of 96 capillary tubes containing the attractant L-aspartate. The effect of bacterial concentration on the chemotactic response is reported. Such high-throughput assay can be used to characterize bacterial chemotaxis function of a wide range of biochemical parameters.

A sensitive, versatile microfluidic assay for bacterial chemotaxis

We have developed a microfluidic assay for bacterial chemotaxis in which a gradient of chemoeffectors is established inside a microchannel via diffusion between parallel streams of liquid in laminar flow. The random motility and chemotactic responses to L-aspartate, L-serine, L-leucine, and Ni(2+) of WT and chemotactic-mutant strains of Escherichia coli were measured. Migration of the cells was quantified by counting the cells accumulating in each of 22 outlet ports. The sensitivity of the assay is attested to by the significant response of WT cells to 3.2 nM L-aspartate, a concentration three orders of magnitude lower than the detection limit in the standard capillary assay. The response to repellents was as robust and easily recorded as the attractant response. A surprising discovery was that L-leucine is sensed by Tar as an attractant at low concentrations and by Tsr as a repellent at higher concentrations. This assay offers superior performance and convenience relative to the existing assays to measure bacterial tactic responses, and it is flexible enough to be used in a wide range of different applications.

Characterizing the adhesion of motile and nonmotile Escherichia coli to a glass surface using a parallel-plate flow chamber

A parallel-plate flow chamber was used to measure the attachment and detachment rates of Escherichia coli to a glass surface at various fluid velocities. The effect of flagella on adhesion was investigated by performing experiments with several E. coli strains: AW405 (motile); HCB136 (nonmotile mutant with paralyzed flagella); and HCB137 (nonmotile mutant without flagella). We compared the total attachment rates and the fraction of bacteria retained on the surface to determine how the presence and movement of the flagella influence transport to the surface and adhesion strength in this dynamic system. At the lower fluid velocities, there was no significant difference in the total attachment rates for the three bacterial strains; nonmotile strains settled at a rate that was of the same order of magnitude as the diffusion rate of the motile strain. At the highest fluid velocity, the effect of settling was minimized to better illustrate the importance of motility, and the attachment rates of both nonmotile strains were approximately five times slower than that of the motile bacteria. Thus, different processes controlled the attachment rate depending on the parameter regime in which the experiment was performed. The fractions of motile bacteria retained on the glass surface increased with increasing velocity, whereas the opposite trend was found for the nonmotile strains. This suggests that the rotation of the flagella enables cells to detach from the surface (at the lower fluid velocities) and strengthens adhesion (at higher fluid velocities), whereas nonmotile cells detach as a result of shear. There was no significant difference in the initial attachment rates of the two nonmotile species, which suggests that merely the presence of flagella was not important in this stage of biofilm development.